AFNI Message Board

History of AFNI updates  

|
October 29, 2021 07:52AM
A cheating method to consider: use the output of adjunct_aw_tableize_roi_info.py, which is a supplementary program used by @animal_warper. ***Note***: this "adjunct" program can change at any point at the cruel whim of developers (hence the 'adjunct' naming convention). But, it probably provides what you want.

If you have used @animal_warper (and you have!), you know that the QC/ dir contains report*.1D files about mapped atlas and template regions, to compare their before- and after-warping volumes. The output table looks something like this:
#  A atlas dset            : CHARM_in_sub-01_anat.nii.gz[4]
#  A mask dset             : sub-01_anat_mask.nii.gz
#  B atlas dset            : /data/demos/setup_MACAQUE_DEMO/MACAQUE_DEMO_REST/NMT_v2.1_sym/NMT_v2.1_sym_05mm/CHARM_in_NMT_v2.1_sym_05mm.nii.gz[4]
#  B mask dset             : /data/demos/setup_MACAQUE_DEMO/MACAQUE_DEMO_REST/NMT_v2.1_sym/NMT_v2.1_sym_05mm/NMT_v2.1_sym_05mm_brainmask.nii.gz
#  Mode_smooth size (nvox) : 1
#  A vox dims (mm)         : 0.500, 0.500, 0.500
#  B vox dims (mm)         : 0.500, 0.500, 0.500
#  A mask Nvox             :    800405
#  B mask Nvox             :    726796
#  A mask volume (mm^3)    :    100050.625
#  B mask volume (mm^3)    :     90849.500
#  MaskVol_A / MaskVol_B   :         1.101
#  A atlas Nroi            :       176
#  B atlas Nroi            :       176
#  Nroi difference         :         0
#  
# ==========================================================================================================================================
# -- KEY --
#  
#  ROI_value     = integer value of ROI
#  Nvox_A        = number of voxels in ROI in dset A
#  Nvox_B        = number of voxels in ROI in dset B
#  Vol_A         = ROI volume in dset A (mm^3)
#  Vol_B         = ROI volume in dset B (mm^3)
#  RelVol_A2B    = relative ROI volume, Vol_A / Vol_B
#  Frac_A        = ROI mask fraction, Vol_A / MaskVol_A
#  Frac_B        = ROI mask fraction, Vol_B / MaskVol_B
#  RelFrac_A2B   = relative ROI mask fraction, Frac_A / Frac_B
#  Label_str     = string label of ROI (if present)
#  
# ==========================================================================================================================================
#    ROI_value        Nvox_A        Nvox_B         Vol_A         Vol_B    RelVol_A2B        Frac_A        Frac_B   RelFrac_A2B     Label_str
# ------------  ------------  ------------  ------------  ------------  ------------  ------------  ------------  ------------  ------------
             4           781           703        97.625        87.875         1.111     9.758e-04     9.673e-04         1.009  #  CL_area_32
             5           273           273        34.125        34.125         1.000     3.411e-04     3.756e-04         0.908  #  CL_area_25
             7           767           729        95.875        91.125         1.052     9.583e-04     1.003e-03         0.955  #  CL_area_24a/b
            10          1924          1589       240.500       198.625         1.211     2.404e-03     2.186e-03         1.099  #  CL_area_24c
            12           451           563        56.375        70.375         0.801     5.635e-04     7.746e-04         0.727  #  CL_area_24a/b_prime
            15          1283           930       160.375       116.250         1.380     1.603e-03     1.280e-03         1.253  #  CL_area_24c_prime
            18          1685          1821       210.625       227.625         0.925     2.105e-03     2.506e-03         0.840  #  CL_area_10
            22           515           538        64.375        67.250         0.957     6.434e-04     7.402e-04         0.869  #  CL_area_14
            27          1123          1104       140.375       138.000         1.017     1.403e-03     1.519e-03         0.924  #  CL_area_11
            30          3123          3327       390.375       415.875         0.939     3.902e-03     4.578e-03         0.852  #  CL_area_13
            34          1486          1189       185.750       148.625         1.250     1.857e-03     1.636e-03         1.135  #  CL_area_12m/o
Note how the first and last columns provide the info you want: the ROI value of any non-empty ROI and its string label, respectively.

The usage for the simple script is:
Takes >= 6 arguments: 
   1) an output file name;
   2) an (warped) atlas of interest, with subbrick selector, if necessary;
   3) a mask for the (warped) atlas (same grid)
   4) a reference atlas (i.e., same one but unwarped), with (same) 
      subbrick selector, if necessary.
   5) a mask for the reference atlas (same grid)
   6) a "modesmooth" value, from modal smoothing used after warping

So, you could use it like:
adjunct_aw_tableize_roi_info.py OUTPUT.1D  DSET_ROI DSET_MASK DSET_ROI DSET_MASK 0
Note how DSET_ROI and DSET_MASK are duplicated (and yes, you need each---this is a simple program with non-optional usage of command line args). The final modesmooth value doesn't matter in this case, so 0 should be fine.

After you output this, you could extract the first and last columns of non-commented values.

--pt
Subject Author Posted

List of clusters/ROIs

Pawel October 28, 2021 01:59PM

Re: List of clusters/ROIs

Daniel Glen October 28, 2021 02:31PM

Re: List of clusters/ROIs

Pawel October 28, 2021 02:43PM

Re: List of clusters/ROIs

Pawel October 28, 2021 03:49PM

Re: List of clusters/ROIs

Pawel October 28, 2021 04:15PM

Re: List of clusters/ROIs

Daniel Glen October 28, 2021 06:56PM

Re: List of clusters/ROIs

Pawel October 28, 2021 08:01PM

Re: List of clusters/ROIs

ptaylor October 29, 2021 07:52AM

Re: List of clusters/ROIs

Pawel October 29, 2021 03:50PM



Sorry, only registered users may post in this forum.

Click here to login